Randomizing genome-scale metabolic networks

Details Randomizing genome-scale metabolic networks Randomizing genome-scale metabolic networks

2010-12-07

arxiv.org/abs/1012.1473v2

PLoS ONE (2011) 6(7):e22295

Biology

Quantitative Biology

Molecular Networks

30 Pages, 6 Main Figures, 6 Supplementary Figures, 1 Supplementary Table

Scientific paper

10.1371/journal.pone.0022295

Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the network is not statistically different from expected in a motivated ensemble. However, when dealing with metabolic networks, the randomization of the network using edge exchange generates fictitious reactions that are biochemically meaningless. Here we provide several natural ensembles of randomized metabolic networks. A first constraint is to use valid biochemical reactions. Further constraints correspond to imposing appropriate functional constraints. We explain how to perform these randomizations with the help of Markov Chain Monte Carlo (MCMC) and show that they allow one to approach the properties of biological metabolic networks. The implication of the present work is that the observed global structural properties of real metabolic networks are likely to be the consequence of simple biochemical and functional constraints.

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